Documentation

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Publication Details

Results for Trost2022:

Summary

Title	Genomic architecture of autism from comprehensive whole-genome sequence annotation
Authors	Trost, B., Thiruvahindrapuram, B., Chan, A.J.S., Engchuan, W., Higginbotham, E.J., Howe, J.L., Loureiro, L.O., Reuter, M.S., Roshandel, D., Whitney, J., Zarrei, M., Bookman, M., Somerville, C., Shaath, R., Abdi, M., Aliyev, E., Patel, R.V., Nalpathamkalam, T., Pellecchia, G., Hamdan, O., Kaur, G., Wang, Z., MacDonald, J.R., Wei, J., Sung, W.W.L., Lamoureux, S., Hoang, N., Selvanayagam, T., Deflaux, N., Geng, M., Ghaffari, S., Bates, J., Young, E.J., Ding, Q., Shum, C., D’Abate, L., Bradley, C.A., Rutherford, A., Aguda, V., Apresto, B., Chen, N., Desai, S., Du, X., Fong, M.L.Y., Pullenayegum, S., Samler, K., Wang, T., Ho, K., Paton, T., Pereira, S.L., Herbrick, J.-A., Wintle, R.F., Fuerth, J., Noppornpitak, J., Ward, H., Magee, P., Baz, A.A., Kajendirarajah, U., Kapadia, S., Vlasblom, J., Valluri, M., Green, J., Seifer, V., Quirbach, M., Rennie, O., Kelley, E., Masjedi, N., Lord, C., Szego, M.J., Zawati, M.H., Lang, M., Strug, L.J., Marshall, C.R., Costain, G., Calli, K., Iaboni, A., Yusuf, A., Ambrozewicz, P., Gallagher, L., Amaral, D.G., Brian, J., Elsabbagh, M., Georgiades, S., Messinger, D.S., Ozonoff, S., Sebat, J., Sjaarda, C., Smith, I.M., Szatmari, P., Zwaigenbaum, L., Kushki, A., Frazier, T.W., Vorstman, J.A.S., Fakhro, K.A., Fernandez, B.A., Lewis, M.E.S., Weksberg, R., Fiume, M., Yuen, R.K.C., Anagnostou, E., Sondheimer, N., Glazer, D., Hartley, D.M., Scherer, S.W.
Technology	WGS
Variant source	Supplemental Table S2C
Cohorts	MSSNG, SSC
Design	simplex, multiplex
URL	https://dx.doi.org/10.1016/j.cell.2022.10.009
Pubmed	36368308
Subject count	15960 The number of subjects for this study could not be determined directly from the variant data; the value given is that reported by the authors in the publication.
Variant event count	144111
Curation notes	View

Breakdown by exonic function

Function	Variant Count
frameshift deletion	800
frameshift insertion	356
frameshift substitution	22
nonframeshift deletion	208
nonframeshift insertion	60
nonframeshift substitution	82
nonsynonymous SNV	13041
other	122723
splicing	396
stopgain	962
stoploss	15
synonymous SNV	5368
unknown	124

What am I looking at?

Summary: Information from the literature piece (e.g. Author, Publisher, DOI) and the study experimental design (e.g. sample size, source of probands, sequencing technology.) For a full list of sources of variants, be sure to check out the publications page. Documentation and description of our work can be found on the help page.

Breakdown by exonic function: We annotated the variants with an effect prediction using ANNOVAR. The functions are categories of variants, such as frameshift variants (i.e. frameshift_elongation (SO:0001909)), loss/gain of stop codon, SNVs and non-frameshift variants. See the full list of possible annotations for exonic variants in the documentation.